Thermodynamic insights into the self-assembly of capped nanoparticles using molecular dynamic simulations

2015 ◽  
Vol 17 (5) ◽  
pp. 3820-3831 ◽  
Author(s):  
André F. de Moura ◽  
Kalil Bernardino ◽  
Cleocir J. Dalmaschio ◽  
Edson R. Leite ◽  
Nicholas A. Kotov
Keyword(s):  
Molecular Modeling ◽  
Molecular Dynamic ◽  
Self Assembly ◽  
The Self ◽  
Molecular Dynamic Simulations ◽  
Research Issue ◽  
Dynamic Simulations ◽  
Self Assembling ◽  
Challenging Research

Although the molecular modeling of self-assembling processes stands as a challenging research issue, there have been a number of breakthroughs in recent years.

Symmetrical Tris(4,6-diamino-5-methylene-2-pyrimidones): New Building Blocks for Self-Assembly of Hollow Spherical Supramolecules Locked by Hydrogen Bonds

1996 ◽  
Vol 61 (10) ◽  
pp. 1464-1472 ◽  
Author(s):  
Daniel Alexander ◽  
Petr Holý ◽  
Pavel Fiedler ◽  
Zdeněk Havlas ◽  
Jiří Závada
Keyword(s):  
Molecular Modeling ◽  
Hydrogen Bonds ◽  
Gas Phase ◽  
Self Assembly ◽  
Building Blocks ◽  
The Self ◽  
Circumstantial Evidence ◽  
Self Assembling ◽  
Molecular Modeling Study ◽  
Modeling Study

Concise synthesis of the tris(pyrimidones) 1a,b is described. Molecular modeling study demonstrated that both the prepared models 1a,b are capable of self-assembling under formation of spherical dimers locked by 18 hydrogen bonds. Extreme insolubility in all common solvents precluded investigation of the self-assembly in solution. Circumstantial evidence in favor of the self-assembly has been provided in the solid and gas phase.

scholarly journals Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study

2018 ◽  
Vol 19 (9) ◽  
pp. 2772 ◽  
Author(s):  
Jean Crowet ◽  
Mehmet Nasir ◽  
Nicolas Dony ◽  
Antoine Deschamps ◽  
Vincent Stroobant ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Molecular Dynamic ◽  
Beta Sheets ◽  
Dynamics Simulation ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Amphipathic Peptide ◽  
Self Assembling ◽  
Ordered Nanostructures

By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called “peptergents”) have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with “peptergency” properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for “peptergency”.

scholarly journals Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries

2017 ◽  
Vol 15 (31) ◽  
pp. 6541-6547 ◽  
Author(s):  
I. R. Sasselli ◽  
I. P. Moreira ◽  
R. V. Ulijn ◽  
T. Tuttle
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Self Assembly ◽  
Peptide Libraries ◽  
Coarse Grained ◽  
Molecular Dynamic Simulations ◽  
New Materials ◽  
Dynamic Simulations ◽  
Dynamics Simulations

Coarse grained molecular dynamic simulations demonstrate that interactions between species in dynamic peptide libraries can cause a disrupting self-assembly effect that affects the possible discovery of new materials.

Molecular Dynamic Simulations of Self-Assembly of Amphiphilic Comb-like Anionic Polybenzoxazines

Langmuir ◽  
2014 ◽  
Vol 30 (40) ◽  
pp. 11858-11865 ◽  
Author(s):  
Riyad Mahfud ◽  
Daniel Lacks ◽  
Hatsuo Ishida ◽  
Syed Qutubuddin
Keyword(s):  
Molecular Dynamic ◽  
Self Assembly ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations

Self-assembling study of sarcolipin and its mutants in multiple molecular dynamic simulations

2017 ◽  
Vol 85 (6) ◽  
pp. 1065-1077 ◽  
Author(s):  
Yipeng Cao ◽  
Xue Wu ◽  
Rui Yang ◽  
Xinyu Wang ◽  
Haiying Sun ◽  
...  
Keyword(s):  
Molecular Dynamic ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Self Assembling

scholarly journals Novel Sulfonamide-Based Carbamates as Selective Inhibitors of BChE

2021 ◽  
Vol 22 (17) ◽  
pp. 9447
Author(s):  
Pratibha Magar ◽  
Oscar Parravicini ◽  
Šárka Štěpánková ◽  
Katarina Svrčková ◽  
Adriana D. Garro ◽  
...  
Keyword(s):  
Quantum Theory ◽  
Molecular Modeling ◽  
Molecular Dynamic ◽  
Active Site ◽  
Inhibitory Activity ◽  
Selectivity Index ◽  
Molecular Dynamic Simulations ◽  
Selective Inhibitors ◽  
Dynamic Simulations

A series of 14 target benzyl [2-(arylsulfamoyl)-1-substituted-ethyl]carbamates was prepared by multi-step synthesis and characterized. All the final compounds were tested for their ability to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) in vitro, and the selectivity index (SI) was determined. Except for three compounds, all compounds showed strong preferential inhibition of BChE, and nine compounds were even more active than the clinically used rivastigmine. Benzyl {(2S)-1-[(2-methoxybenzyl)sulfamoyl]-4-methylpentan-2-yl}carbamate (5k), benzyl {(2S)-1-[(4-chlorobenzyl)sulfamoyl]-4-methylpentan-2-yl}carbamate (5j), and benzyl [(2S)-1-(benzylsulfamoyl)-4-methylpentan-2-yl]carbamate (5c) showed the highest BChE inhibition (IC50 = 4.33, 6.57, and 8.52 µM, respectively), indicating that derivatives 5c and 5j had approximately 5-fold higher inhibitory activity against BChE than rivastigmine, and 5k was even 9-fold more effective than rivastigmine. In addition, the selectivity index of 5c and 5j was approx. 10 and that of 5k was even 34. The process of carbamylation and reactivation of BChE was studied for the most active derivatives 5k, 5j. The detailed information about the mode of binding of these compounds to the active site of both BChE and AChE was obtained in a molecular modeling study. In this study, combined techniques (docking, molecular dynamic simulations, and QTAIM (quantum theory of atoms in molecules) calculations) were employed.

Directive Effect of Chain Length in Modulating Peptide Nano-assemblies

2020 ◽  
Vol 27 (9) ◽  
pp. 923-929
Author(s):  
Gaurav Pandey ◽  
Prem Prakash Das ◽  
Vibin Ramakrishnan
Keyword(s):  
Electron Microscopy ◽  
Amino Acids ◽  
Light Scattering ◽  
Chain Length ◽  
Self Assembly ◽  
The Self ◽  
Ionic Charge ◽  
Self Assembling ◽  
Biophysical Techniques

Background: RADA-4 (Ac-RADARADARADARADA-NH2) is the most extensively studied and marketed self-assembling peptide, forming hydrogel, used to create defined threedimensional microenvironments for cell culture applications. Objectives: In this work, we use various biophysical techniques to investigate the length dependency of RADA aggregation and assembly. Methods: We synthesized a series of RADA-N peptides, N ranging from 1 to 4, resulting in four peptides having 4, 8, 12, and 16 amino acids in their sequence. Through a combination of various biophysical methods including thioflavin T fluorescence assay, static right angle light scattering assay, Dynamic Light Scattering (DLS), electron microscopy, CD, and IR spectroscopy, we have examined the role of chain-length on the self-assembly of RADA peptide. Results: Our observations show that the aggregation of ionic, charge-complementary RADA motifcontaining peptides is length-dependent, with N less than 3 are not forming spontaneous selfassemblies. Conclusion: The six biophysical experiments discussed in this paper validate the significance of chain-length on the epitaxial growth of RADA peptide self-assembly.

Self-assembling behaviour of a modified aromatic amino acid in competitive medium

Soft Matter ◽  
2020 ◽  
Vol 16 (28) ◽  
pp. 6599-6607 ◽  
Author(s):  
Pijush Singh ◽  
Souvik Misra ◽  
Nayim Sepay ◽  
Sanjoy Mondal ◽  
Debes Ray ◽  
...  
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Aromatic Amino Acid ◽  
Photophysical Properties ◽  
Solvent Mixture ◽  
The Self ◽  
Solvent Ratio ◽  
Self Assembling

The self-assembly and photophysical properties of 4-nitrophenylalanine (4NP) are changed with the alteration of solvent and final self-assembly state of 4NP in competitive solvent mixture and are dictated by the solvent ratio.

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